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Welcome to ProPhyle

ProPhyle brings metagenomic classification from clusters to laptops. This is possible thanks to a novel indexing strategy,
based on the bottom-up propagation of k-mers in the phylogenetic/taxonomic tree, assembling contigs at each node and matching using a full-text search.

Compared to other state-of-the-art classifiers, ProPhyle provides several unique features:

Flexibility. ProPhyle is easy to use with any user-provided phylogenetic trees and reference genomics sequences (e.g., reads or assemblies). It can classify short reads, long reads, or even assembled contigs.

Standard bioinformatics formats. Newick/NHX is used for representing phylogenetic trees and SAM/BAM for reporting assignments.

Lossless k-mer indexing. ProPhyle stores a list of all genomes containing a k-mer. The classification is, therefore, accurate even with trees containing similar genomes (e.g, phylogenetic trees for a single species).

[1] is the main reference for the entire ProPhyle package. [2] contains a summary of the ProPhyle algorithm, [3] provides a thorough description (see Chapter 12), and [4] explains details of the BWT-indexing technique.